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Adds missing ENDMDL on HETATM in pdb_tidy
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PR #161
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@joaomcteixeira
joaomcteixeira authored Dec 13, 2023
2 parents 34a32b6 + 402f88e commit 97de57d
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Showing 3 changed files with 78 additions and 6 deletions.
12 changes: 6 additions & 6 deletions pdbtools/pdb_tidy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -214,9 +214,9 @@ def make_TER(prev_line):
if atom_section:
atom_section = False
yield make_TER(prev_line)
if in_model:
yield "{:<80}\n".format("ENDMDL")
in_model = False
if in_model:
yield "{:<80}\n".format("ENDMDL")
in_model = False

if line.startswith('MODEL'):
line = "MODEL " + " " + str(num_models).rjust(4)
Expand All @@ -240,9 +240,9 @@ def make_TER(prev_line):
# Add last TER statement
atom_section = False
yield make_TER(prev_line)
if in_model:
yield "{:<80}\n".format("ENDMDL")
in_model = False
if in_model:
yield "{:<80}\n".format("ENDMDL")
in_model = False

# Add END statement
yield "{:<80}\n".format("END")
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45 changes: 45 additions & 0 deletions tests/data/hetatm_ensemble.pdb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
MODEL 1
HETATM 1 C1 G39 B 500 -30.374 -53.143 6.122 1.00 31.18 C
HETATM 2 O1A G39 B 500 -31.439 -52.533 5.850 1.00 30.30 O
HETATM 3 O1B G39 B 500 -29.257 -52.625 5.879 1.00 31.23 O
HETATM 4 C2 G39 B 500 -30.437 -54.486 6.725 1.00 30.48 C
HETATM 5 C3 G39 B 500 -29.159 -55.188 7.132 1.00 30.04 C
HETATM 6 C4 G39 B 500 -29.380 -56.162 8.294 1.00 30.37 C
HETATM 7 N4 G39 B 500 -28.195 -56.994 8.430 1.00 30.09 N1+
HETATM 8 C5 G39 B 500 -30.627 -57.033 8.097 1.00 29.53 C
HETATM 9 N5 G39 B 500 -30.803 -57.955 9.206 1.00 28.16 N
HETATM 10 C6 G39 B 500 -31.883 -56.178 7.937 1.00 30.53 C
HETATM 11 C7 G39 B 500 -31.632 -55.093 6.901 1.00 30.75 C
HETATM 12 O7 G39 B 500 -33.007 -56.989 7.531 1.00 31.80 O
HETATM 13 C8 G39 B 500 -34.158 -56.905 8.398 1.00 30.52 C
HETATM 14 C9 G39 B 500 -34.879 -55.553 8.283 1.00 31.36 C
HETATM 15 C10 G39 B 500 -30.683 -59.283 9.087 1.00 27.13 C
HETATM 16 O10 G39 B 500 -30.629 -59.863 8.010 1.00 26.14 O
HETATM 17 C11 G39 B 500 -30.611 -60.040 10.380 1.00 26.05 C
HETATM 18 C81 G39 B 500 -35.153 -58.020 8.079 1.00 29.88 C
HETATM 19 C82 G39 B 500 -34.654 -59.395 8.467 1.00 28.23 C
HETATM 20 C91 G39 B 500 -35.425 -55.279 6.891 1.00 32.33 C
ENDMDL
MODEL 2
HETATM 1 C1 G39 B 500 -30.374 -53.143 6.122 1.00 31.18 C
HETATM 2 O1A G39 B 500 -31.439 -52.533 5.850 1.00 30.30 O
HETATM 3 O1B G39 B 500 -29.257 -52.625 5.879 1.00 31.23 O
HETATM 4 C2 G39 B 500 -30.437 -54.486 6.725 1.00 30.48 C
HETATM 5 C3 G39 B 500 -29.159 -55.188 7.132 1.00 30.04 C
HETATM 6 C4 G39 B 500 -29.380 -56.162 8.294 1.00 30.37 C
HETATM 7 N4 G39 B 500 -28.195 -56.994 8.430 1.00 30.09 N1+
HETATM 8 C5 G39 B 500 -30.627 -57.033 8.097 1.00 29.53 C
HETATM 9 N5 G39 B 500 -30.803 -57.955 9.206 1.00 28.16 N
HETATM 10 C6 G39 B 500 -31.883 -56.178 7.937 1.00 30.53 C
HETATM 11 C7 G39 B 500 -31.632 -55.093 6.901 1.00 30.75 C
HETATM 12 O7 G39 B 500 -33.007 -56.989 7.531 1.00 31.80 O
HETATM 13 C8 G39 B 500 -34.158 -56.905 8.398 1.00 30.52 C
HETATM 14 C9 G39 B 500 -34.879 -55.553 8.283 1.00 31.36 C
HETATM 15 C10 G39 B 500 -30.683 -59.283 9.087 1.00 27.13 C
HETATM 16 O10 G39 B 500 -30.629 -59.863 8.010 1.00 26.14 O
HETATM 17 C11 G39 B 500 -30.611 -60.040 10.380 1.00 26.05 C
HETATM 18 C81 G39 B 500 -35.153 -58.020 8.079 1.00 29.88 C
HETATM 19 C82 G39 B 500 -34.654 -59.395 8.467 1.00 28.23 C
HETATM 20 C91 G39 B 500 -35.425 -55.279 6.891 1.00 32.33 C
ENDMDL
END
27 changes: 27 additions & 0 deletions tests/test_pdb_tidy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -260,6 +260,33 @@ def test_corrects_model_ENDMDL(self):
self.assertEqual(self.stdout[-1].strip(), "END")
self.assertEqual(len(self.stdout[-1]), 80)

def test_corrects_model_ENDMDL_with_HETATM(self):
"""Correct MODEL lines."""
fpath = os.path.join(data_dir, 'hetatm_ensemble.pdb')
sys.argv = ['', fpath]
self.exec_module()
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 45)
self.assertEqual(len(self.stderr), 0)

# MODEL lines
self.assertEqual(len(self.stdout[0]), 80)
self.assertEqual(len(self.stdout[0].strip()), 14)
self.assertEqual(len(self.stdout[22]), 80)
self.assertEqual(len(self.stdout[22].strip()), 14)
self.assertEqual(self.stdout[0].strip(), "MODEL 1")
self.assertEqual(self.stdout[22].strip(), "MODEL 2")

# ENDMDL LINES
self.assertEqual(len(self.stdout[21]), 80)
self.assertEqual(len(self.stdout[43]), 80)
self.assertEqual(self.stdout[21].strip(), "ENDMDL")
self.assertEqual(self.stdout[43].strip(), "ENDMDL")

# END LINES
self.assertEqual(self.stdout[-1].strip(), "END")
self.assertEqual(len(self.stdout[-1]), 80)


def test_file_not_found(self):
"""$ pdb_tidy not_existing.pdb"""
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